CSynth

CSynth models three-dimensional chromatin structures from Hi-C and other chromosome conformation capture (3C) data to explore spatial genome organization and its role in gene regulation.

Key Features:

• Restraint-based modelling: Implements a physics-based chromatin restraint modeller that computes 3D genome structures from contact-derived restraints.
• Real-time parameter adjustment: Allows on-the-fly modification of modelling parameters with immediate recomputation of structural models.
• Data integration and comparison: Integrates Hi-C and other 3C technique datasets and supports comparison between models derived from different tissues, cell states, or third-party 3D modelling outputs.

Scientific Applications:

• Gene regulation and expression: Enables analysis of spatial chromatin arrangements relevant to transcriptional regulation.
• Epigenetics: Facilitates examination of three-dimensional interactions underlying epigenetic regulation.
• Developmental biology: Supports investigation of chromatin structural changes across developmental states.
• Disease-related chromatin pathology: Assists study of structural chromatin alterations associated with disease mechanisms.

Methodology:

Uses a physics-based, restraint-driven modelling approach that computes 3D genome structures from chromatin restraints derived from Hi-C and other 3C techniques with real-time parameter updates.